In this paper, hierarchical micro/nano structures composed of periodic microstructures, laser-induced periodic surface structures (LIPSS), and nanoparticles were fabricated by femtosecond laser processing (LP). A layer of hydrophobic species was formed on the micro/nano structures through perfluorosilane modification (PM). The reflectivity and hydrophobicity’s influence mechanisms of structural height, duty cycle, and size are experimentally elucidated. The average reflectivity of the silicon surface in the visible light band is reduced to 3.0% under the optimal parameters, and the surface exhibits a large contact angle of 172.3 ± 0.8° and a low sliding angle of 4.2 ± 1.4°. Finally, the durability of the anti-reflection and superhydrophobicity is also confirmed. This study deepens our understanding of the principles of anti-reflection and superhydrophobicity and expands the design and preparation methods for self-cleaning and anti-reflective surfaces.